About Epigenetic Analysis

Providing hands-on support from epigenome research design to publication/productization

Our epigenome-specialized analytical team provides hands-on support from designing experiments to, publication and productization. From 2017 to 2018, we have been involved in 38 epigenome research projects, three of which were published on international journal. We offer the optimal plan based on the customers’ purpose, budget and period for each research project.

Pricing for Epigenetic Research
Plan2 times/month4 times/month6 times/month8 times/month
Consulting ONLY$1,900$3,400$4,600$5,300
Consulting and Analysis$2,900$2,900$7,400$9,100

* 30% discount for academic use

Hands-on support for publication

Article title: Dynamically and epigenetically coordinated GATA / ETS / SOX transcription factor expression is indispensable for endothelial cell differentiation.

Publication journal: Nucleic Acids Res. 2017 May 5; 45 (8): 4344-4358. Doi: 10.1093 / nar / gkx 159.

Summary: To elucidate the mechanism of epigenetic control in angiogenesis, we exposed ESC to VEGF that enhanced the growth of vascular endothelial cells and determined the changes in transcriptome using RNA-seq and ChIP-seq data. By narrowing down the transcription factors and experimentally verifying them, we clarified the functions of notable transcription factor and their cooperative interactions against other factors.

Our support: Designing experiment, analyzing raw data, and providing visualized data

Creating Figures and Tables

All images and illustrations used on our website are original works. In accordance with journals and other usage, we create visualized data.
Please contact us regarding the pricing.

Transcriptome Analysis

By analyzing the mRNA expression level (via RNA-seq data), it is possible to define a specific cell state and to narrow down the genes involved in the maintenance and direction of cell fate. Gene expression level is evaluated by FKPM (fragments per kilobase of exon per million mapped reads) or read count. Which value to evaluate depends on the experimental protocol and the research purpose. Using RNA-seq also helps to characterize non-coding RNA, identify somatic mutations and germline mutations, and predict splicing variants.

PlanDelivery dateCost/Sample
(1~4 Samples)
(5~12 Samples)
(13~24 Samples)
(>25 Samples)
RNA-seq Experiment and Analysis8〜10 weeks$2,500$2,300$2,100$1,900
RNA-seq Experiment ONLY8〜10 weeks$2,300$2,100$1,900$1,700
RNA-seq Analysis ONLY2 weeks$950$750$550$400

Open Chromatin Analysis

Methods such as ATAC-seq, DNase-seq, FAIRE-seq, allow us to predict the open chromatin region at genome-wide level. This is particularly important for assessing which nucleosome-free region a transcription factor and other factors may bind. By analyzing the open chromatin region in specific cells, we can narrow down the transcription factors that play a major role in regulating expression level of corresponding genes. The open chromatin region can be common in a group of cells or be strictly regulated in a specific cell (or during cell fate) to which the accessibility of enhancers and promoters may be altered. Transcription factors that play a cell-specific role are known to bind to enhancers, and transcription factors can be predicted by performing binding motif analysis of cell-specific enhancer sites. Although ATAC-seq and DNase-seq do not make use of antibody for immunoprecipitation, these techniques can perform footprint analysis, predicting the binding region of the transcription factor at single nucleotide level.

PlanDelivery DateCost/Sample
(1~4 Samples)
(5~12 Samples)
(13~24 Samples)
(>25 Samples)
ATAC-seq Experiment and Analysis8〜10 weeks$4,700$4,300$4,000$3,800
ATAC-seq Experiment ONLY8〜10 weeks$3,300 $2,800$2,500$2,300
ATAC-seq Analysis ONLY2 weeks$1,900 $1,300$1,000$950

*Please contact us regarding the pricing and the type of the sample as the process of experimental analysis may vary (cultured cell, tissue, etc.)

Genome-Wide Interaction Analysis

By using HiC or ChIA – PET, it is possible to detect genomic-wide chromatin interactions. Expression of genes is thought to be regulated by the interaction between enhancer and promoter, and the combination is regulated by the three-dimensional structure of the genome. The basic structural unit capable of interacting with an enhancer or promoter is called a topology associating domain (TAD). HiC and ChIA-PET can predict the combination and the position of enhancers and promoters by clarifying the position and the range of cell-specific TAD. Please contact us as the analysis cost varies depending on the number of data and the content itself.

Genome-Wide DNA Methylation Analysis

Bisulfite treatment allows non-methylated cytosine to be converted into uracil. This method along with NGS helps identify the location of methylated site within DNA at single nucleotide resolution. There are two notable techniques in analyzing genome-wide DNA methylation level: 1) RRBS (reduced representation bisulfite sequencing) and 2) WGBS (whole-genome bisulfite sequencing). RRBS uses restriction enzymes to selectively cleave CpG sites within DNA for methylation analysis, whereas WGBS, as the name suggests, locates the methylation sites for all regions. While WGBS has the advantage of being able to analyze at the whole genome level, it is relatively more as it requires more reads than RRBS.

By comparing DNA methylation data with different conditions, we are able to predict regions where DNA methylation is induced (hindering gene expression) or suppressed (genes properly expressed).